RetrogeneDB ID: retro_ocun_1562

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:766133..767157(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027525
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CKB
• Ensembl ID: ENSOCUG00000008818
• Aliases: None
• Description: creatine kinase, brain (CKB), mRNA [Source:RefSeq mRNA;Acc:NM_001082261]

Sequence

>retro_ocun_1562
GAGCTGCGTGCCAAGAGCATGCCCAGCGGCTTCACGCTGGACTTCGTCATCCAGACCGGCGTCGACAACCCGGGCCACCC
GTACATCATGACCGTGGGCTGCGTGGCGAGCGACGAGGAGTCCTTCGAGGTGTTCAGGGAGCTCTTTGACCCCATCATCG
AGGACCGGCAGGGCGACTACAAGCCCAGCGACGAACGCAAGACCGACCTCAACCCCGACAACCTGCAGGGCGGCGACAAC
CTGGACCCTAACTACGTGCTGAGCTCGCGGGTGCACACTGGCCGGAGCATCCGTGGCTTCTGCCTGCCCCCACACTGCAG
CCGCGGTGAGCACCCAGCCATAGAGAAGCTGGCGGTGGAAGCGCTGTCCAGCCTGGACAGCGACCTGGCCGGCAGGTACT
ACGCGCTCAAGAGCATGACTGAGGCGGAGCAGCAGCAGCTTATCAACGACCGCTTTCTCTTCGACAAGCCCGTGTCGCCC
CTGCTGCTGGCCACCGGCATGGCCCACAACTGGCCGGACACCCCGCGGTATTTGGCACAATGATAAGAAGACTTTCCTGG
TGTGGATCAACGAGGAGGACCACCTCCGGGTCATCTCCATTCAGAAGGGAGGGAACATAAAGGAGGTGTTCACCGGCTTC
TGCAATGGCCTCACCCAGATTGAAACTCTCTTCAAGTCTAAGAACTATGAGTTCATGTGGAACCCTCACCTGGGCTACAT
CCTCACCTGCCCATCGAACCTGGGCACTGGGCTGTGGGCAGGTGCGCACATCAAGCTGCCCCACCTGGGTAAGCACAAGA
AGTTCTCTGAGGTGCTCAAGCGGCTGCAGCTTCAGAAGCGAGGCACAGGTGGTGTGGACACGGCTGCCGTGGGCGGGGTC
TTTGACGTCTTCAACGCCGACAGCCTGGGCTTCTCCAAGGTGGAGTTGGTGCAGATGGTGGTGGATAGTGTGAAGCCGCT
CATTGAGATGCAGCAGCGGCTGGAGCAGGGCCAGGCCATCAACGACCTCATGCCTGCCCAGAAG

Alignment

ORF - retro_ocun_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 89.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELRAKSTPSGFTLDDVIQTGVDNPGHPFIMTVGCVAGDEESYEVFKELFDPIIEDRHGGYKPSDEHKTDL
          ELRAKS.PSGFTLD.VIQTGVDNPGHP.IMTVGCVA.DEES.EVF.ELFDPIIEDR.G.YKPSDE.KTDL
Retrocopy ELRAKSMPSGFTLDFVIQTGVDNPGHPYIMTVGCVASDEESFEVFRELFDPIIEDRQGDYKPSDERKTDL

Parental  NPDNLQGGDDLDPNYVLSSRVRTGRSIRGFCLPPHCSRGERRAVEKLAVEALSSLDGDLAGRYYALKSMT
          NPDNLQGGD.LDPNYVLSSRV.TGRSIRGFCLPPHCSRGE..A.EKLAVEALSSLD.DLAGRYYALKSMT
Retrocopy NPDNLQGGDNLDPNYVLSSRVHTGRSIRGFCLPPHCSRGEHPAIEKLAVEALSSLDSDLAGRYYALKSMT

Parental  EAEQQQLIDDHFLFDKPVSPLLLASGMARDWPDA-RGIWHNDNKTFLVWINEEDHLRVISMQKGGNMKEV
          EAEQQQLI.D.FLFDKPVSPLLLA.GMA..WPD..RGIWHND.KTFLVWINEEDHLRVIS.QKGGN.KEV
Retrocopy EAEQQQLINDRFLFDKPVSPLLLATGMAHNWPDT>RGIWHNDKKTFLVWINEEDHLRVISIQKGGNIKEV

Parental  FTRFCNGLTQIETLFKSKNYEFMWNPHLGYILTCPSNLGTGLRAGVHIKLPHLGQHEKFSEVLKRLRLQK
          FT.FCNGLTQIETLFKSKNYEFMWNPHLGYILTCPSNLGTGL.AG.HIKLPHLG.H.KFSEVLKRL.LQK
Retrocopy FTGFCNGLTQIETLFKSKNYEFMWNPHLGYILTCPSNLGTGLWAGAHIKLPHLGKHKKFSEVLKRLQLQK

Parental  RGTGGVDTAAVGGVFDVSNADRLGFSEVELVQMVVDGVKLLIEMEQRLEQGQAIDDLMPAQK
          RGTGGVDTAAVGGVFDV.NAD.LGFS.VELVQMVVD.VK.LIEM.QRLEQGQAI.DLMPAQK
Retrocopy RGTGGVDTAAVGGVFDVFNADSLGFSKVELVQMVVDSVKPLIEMQQRLEQGQAINDLMPAQK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.50 RPM	1086.93 RPM
SRP017611_kidney	0.10 RPM	112.30 RPM
SRP017611_liver	0.00 RPM	2.54 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1562 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1562 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018277	5 retrocopies	retro_cfam_1828, retro_cfam_2061, retro_cfam_2159, retro_cfam_274, retro_cfam_664,
Ciona intestinalis	ENSCING00000007141	1 retrocopy	retro_cint_27,
Macropus eugenii	ENSMEUG00000002979	3 retrocopies	retro_meug_1069, retro_meug_1569, retro_meug_2156,
Oryctolagus cuniculus	ENSOCUG00000008818	1 retrocopy	retro_ocun_1562 ,
Sarcophilus harrisii	ENSSHAG00000016459	2 retrocopies	retro_shar_432, retro_shar_645,